|
| Status |
Public on Feb 02, 2011 |
| Title |
H3_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Leaf tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Columbia 2x
tissue: rosette leaf
stage: Rosette leaves prior to bolting
antibody: H3
antibody vendor: Abcam
antibody catalog #: Ab1791
antibody lot #: 608451
|
| Growth protocol |
Plants were grown in vermiculite mixed with 30% soil in a growth chamber with growth conditions of 22°/18° C (day/night) and 16 hr of illumination per day.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For immunoprecipitation, 2 ug H3-core (Ab1791; Abcam, Cambridge, MA), 4 ug H3K4me3 (Ab8580) or 3.6 ug H3K9ac (Ab10812) antibodies were added to 600 ul diluted chromatin and incubated overnight at 4oC with gentle rotation. Immunoprecipitated chromatin-DNA (IP-DNA) and 50 ul input chromatin-DNA (without IP) were subjected to reverse crosslink and purified for sequencing libraries preparation. ChIP-seq libraries were constructed according to protocols described in Illumina ChIP sequencing kit (Illumina Inc., San Diego, CA). Libraries with a range of 250-300-bp were excised and amplified for subsequent cluster generation and massively parallel sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana (TAIR9, 2008) genomes using home-made perl script. All reads mapping with perfect mach and only once and longer than 40 nt were retained.
|
| |
|
| Submission date |
Jun 10, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Misook Ha |
| E-mail(s) |
misook.ha@gmail.com
|
| Phone |
7732795900
|
| Organization name |
National Heart Lung Blood Institute
|
| Lab |
Laboratory of Epigenome Biology
|
| Street address |
NIH
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9062 |
| Series (1) |
| GSE22276 |
Genome-wide maps of histone modifications in Arabidopsis thaliana |
|
| Relations |
| SRA |
SRX022328 |
| BioSample |
SAMN00015354 |
